[2024-01-24 13:58:56,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:56,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:56,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference
[2024-01-24 13:58:57,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,442] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg04956538-4fa1-444b-a35d-2e0b0797e5ef/GCF_000697965.2_ASM69796v2_genomic.fna.gz | prodigal -d GCF_000697965.2_ASM69796v2_genomic.fna/cds.fna -a GCF_000697965.2_ASM69796v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:20,477] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:20,478] [INFO] Task started: HMMsearch
[2024-01-24 13:59:20,478] [INFO] Running command: hmmsearch --tblout GCF_000697965.2_ASM69796v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/reference_markers.hmm GCF_000697965.2_ASM69796v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:20,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:20,993] [INFO] Found 6/6 markers.
[2024-01-24 13:59:21,056] [INFO] Query marker FASTA was written to GCF_000697965.2_ASM69796v2_genomic.fna/markers.fasta
[2024-01-24 13:59:21,056] [INFO] Task started: Blastn
[2024-01-24 13:59:21,056] [INFO] Running command: blastn -query GCF_000697965.2_ASM69796v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/reference_markers.fasta -out GCF_000697965.2_ASM69796v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:22,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:22,130] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:22,131] [INFO] Target genome list was writen to GCF_000697965.2_ASM69796v2_genomic.fna/target_genomes.txt
[2024-01-24 13:59:22,136] [INFO] Task started: fastANI
[2024-01-24 13:59:22,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg04956538-4fa1-444b-a35d-2e0b0797e5ef/GCF_000697965.2_ASM69796v2_genomic.fna.gz --refList GCF_000697965.2_ASM69796v2_genomic.fna/target_genomes.txt --output GCF_000697965.2_ASM69796v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:47,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:47,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:47,130] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:47,130] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:47,131] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	87.247	1670	2421	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	81.9303	1105	2421	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	81.902	1116	2421	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	81.8791	1136	2421	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	81.6027	1141	2421	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	81.5518	1171	2421	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	81.4544	1164	2421	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	81.3178	1060	2421	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	81.2309	899	2421	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	81.1295	874	2421	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	81.1252	871	2421	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.7663	848	2421	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	80.7548	1006	2421	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	80.6104	1005	2421	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	80.4222	826	2421	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	79.6888	725	2421	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.5426	674	2421	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	79.4812	775	2421	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	79.4646	780	2421	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	79.4461	737	2421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,132] [INFO] DFAST Taxonomy check result was written to GCF_000697965.2_ASM69796v2_genomic.fna/tc_result.tsv
[2024-01-24 13:59:47,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:47,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:47,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/checkm_data
[2024-01-24 13:59:47,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:47,210] [INFO] Task started: CheckM
[2024-01-24 13:59:47,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000697965.2_ASM69796v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000697965.2_ASM69796v2_genomic.fna/checkm_input GCF_000697965.2_ASM69796v2_genomic.fna/checkm_result
[2024-01-24 14:00:50,606] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:50,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:50,633] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:50,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:50,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000697965.2_ASM69796v2_genomic.fna/markers.fasta)
[2024-01-24 14:00:50,634] [INFO] Task started: Blastn
[2024-01-24 14:00:50,634] [INFO] Running command: blastn -query GCF_000697965.2_ASM69796v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ee8c9fe-1765-449c-b313-6858ad238ffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000697965.2_ASM69796v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:52,908] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:52,913] [INFO] Selected 8 target genomes.
[2024-01-24 14:00:52,913] [INFO] Target genome list was writen to GCF_000697965.2_ASM69796v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:52,918] [INFO] Task started: fastANI
[2024-01-24 14:00:52,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg04956538-4fa1-444b-a35d-2e0b0797e5ef/GCF_000697965.2_ASM69796v2_genomic.fna.gz --refList GCF_000697965.2_ASM69796v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000697965.2_ASM69796v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:07,243] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:07,254] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:07,254] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000697965.2	s__Ensifer adhaerens	100.0	2418	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.67	95.82	0.92	0.87	37	conclusive
GCF_016919405.1	s__Ensifer sp000799055	93.0531	1941	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.37	96.05	0.91	0.88	3	-
GCF_002007205.1	s__Ensifer adhaerens_D	91.1807	1918	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940685.1	s__Ensifer adhaerens_E	90.5942	1907	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469595.1	s__Ensifer sp900469595	88.3218	1822	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.13	98.13	0.88	0.88	2	-
GCF_001429285.1	s__Ensifer sp001429285	87.608	1805	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.69	95.18	0.90	0.85	16	-
GCF_001695835.1	s__Ensifer sp001695835	87.4231	1710	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	100.00	100.00	1.00	0.99	4	-
GCF_013283665.1	s__Ensifer sesbaniae	87.2255	1673	2421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.93	98.93	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:07,255] [INFO] GTDB search result was written to GCF_000697965.2_ASM69796v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:07,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:07,260] [INFO] DFAST_QC result json was written to GCF_000697965.2_ASM69796v2_genomic.fna/dqc_result.json
[2024-01-24 14:01:07,260] [INFO] DFAST_QC completed!
[2024-01-24 14:01:07,260] [INFO] Total running time: 0h2m11s